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# UnifiedGenotyper / Strand Bias (SB)

Posts: 3Member
edited January 2013

Hi,

How to get all SNPs variants with Strand Bias (high SB value) ?

GenomeAnalysisTK.jar -T UnifiedGenotyper  \
-R  ucsc.hg19.fasta   -D dbsnp_135.hg19.vcf  \
-stand_emit_conf 1.5 -stand_call_conf 1.5 \
-o Sample_2.snv.vcf  -I Sample_2.recal.bam -nt 10


Thanks,
Q

Post edited by Geraldine_VdAuwera on
Tagged:

You probably want to take a look at SelectVariants:

Geraldine Van der Auwera, PhD

• Posts: 3Member

Hi Geraldine,

Thanks for responding my quesitns. I looked at the 'SelectVariants', which is great option that I will need later on a project. However, what I try to find out is:
How to get all possible variatants (SNP & INDEL) that "GenomeAnalysisTK.jar -T UnifiedGenotyper" detects WITHOUT filter anything. Because the coverage of our sampels are low, thus I want to have as much as sensitive as possible.

Ah, I see -- I misunderstood your original question, sorry. Take a look at the --output_mode argument of the UG, see if that will give you what you want:

Geraldine Van der Auwera, PhD

• Posts: 3Member

Hi Geraldine,

Thanks for the links, its great one. I've tried all the "--output_mode" options
EMIT_VARIANTS_ONLY (default) - doesn't call ALL possible Variants (by verifying with IGV)
EMIT_ALL_CONFIDENT_SITES - Gives similar (little more/less) variants compare with 'EMIT_VARIANTS_ONLY'
EMIT_ALL_SITES - gives every sites (Doesn't make sense for a current project!) I could use "mpilleup" instead if needed.

Overall, I am still struggle with calling all possible variant (regardless any filter!) on a single sample. I like to apply a variant-filter later. Do you a better idea?

Thanks,
Q

• Posts: 684GATK Developer mod

See --standard_min_confidence_threshold_for_calling.

Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

• Posts: 3Member

On my original question, I've palyed with '-stand_emit_conf 1.5 -stand_call_conf 1.5' which allow very low phred score! There must be other factors that interfere the variant calling. I have yet to figure-it-out.

Thanks,
Q